Code chunks

Shortcuts:

• Cmd/Strg+Alt+I: insert new chunk

• Cmd/Strg+Enter: run single line of code

• Cmd/Strg+Shift+Enter: run whole code chunk

• code chunks should be relatively self-contained

  • and focussed on a single task

Chunk labels

• we can give each code chunk specifications using #| directly under ```{r}
  • #| label: simple-math will label the chunk ‘simple-math’

```{r}
#| label: simple-math

4 + 4
```

[1] 8

Advantages of using chunk labels

1. We can navigate to specific code chunks using the drop-down menu in the script editor
2. Graphics (i.e., plots) produced by chunks will have useful names that make it easier to find them later (more on this soon)

Chunk labels should…

• be short and informative
• contain no spaces (use - or _)
• be unique in a document (not repeated)

Chunk options

• chunk output can be formatted with options that tell R what to do with code when rendering your document
  • there are almost 60 options
  • the most important options control if your code chunk is executed when rendering and what results are printed in the output report:
• eval: false prevents code from being printed in rendered output
• include: false runs the code, but doesn’t show the code or results in the final document
• echo: false prevents code, but not the output, from appearing in the rendered output
• message: false or warning: false prevents messages or warnings from appearing in the rendered output
• results: hide hides printed output; fig-show: false hides plots
• error: true renders the document even if errors are encountered

Global options

• the chunk options just mentioned can also be set globally for your whole document by adding them to your YAML under excute:

title: "My report"
execute:
  echo: false

• and then subsequent code chunks can override the global setting in a case-by-case basis

Figures

Figure label

• labels for code chunks that print a figure need to start with fig-
  • the figure will then have a number when printed

```{r}
#| label: fig-flights-dec120

fig_flights
```

Abbildung 2: ?(caption)

Figure caption

• fig-cap: adds a figure caption which will appear in the rendered document
  • always wrap the caption with quotation marks! fig-cap: "..."

```{r}
#| label: fig-flights-dec120-2
#| fig-cap: "Departure delay by arrival delay for December 2013. Airline is indicated via point colour."

fig_flights
```

Abbildung 3: Departure delay by arrival delay for December 2013. Airline is indicated via point colour.

Figure sizing

• a big challenge of graphics in Quarto is getting the figures the right size and shape
• five main chunk options that can be helpful:
  • fig-width: sets the width of the figure in inches (e.g., fig-width = 4)
  • fig-height: sets the height of the figure in inches (e.g., fig-height = 4)
  • fig-asp: sets the aspect-ratio of your figure (if you set only height or width; e.g., fig-asp = 0.618)
  • out-width: sets the width of the figure in percentage to line width (e.g., out-width = "70%")
  • out-height: sets the height of the figure in percentage to line width (e.g., out-height = "30%")
  • fig-align: centre centres the figure on the output page

Tables

• we can print tables as we see them in the console
• we can also add further formatting using the kable() function from the knitr package

df_flights %>% 
  select(1:5) %>% 
  head()

# A tibble: 6 × 5
   year month   day dep_time sched_dep_time
  <dbl> <dbl> <dbl>    <dbl>          <dbl>
1  2013     1     1      517            515
2  2013     1     1      533            529
3  2013     1     1      542            540
4  2013     1     1      544            545
5  2013     1     1      554            600
6  2013     1     1      554            558

df_flights %>% 
  select(1:5) %>% 
  head() %>% 
  knitr::kable()

Table captions

• we can also add a caption to the table using by adding a label and tbl-cap

```{r}
#| output-location: fragment
#| label: tbl-flights
#| tbl-cap: "A table made with `knitr`. The first 6 rows of the first 5 columns from the flights.csv dataset are printed."
df_flights %>% 
  select(1:5) %>% 
  head() %>% 
  knitr::kable(
  )
```

Column names

• lastly, let’s fix the column names

```{r}
#| output-location: fragment
#| label: tbl-flights2
#| tbl-cap: "A table made with `knitr`. The first 6 rows of the first 5 columns from the flights.csv dataset are printed."
df_flights %>% 
  select(1:5) %>% 
  head() %>% 
  knitr::kable(
    col.names = c("Year", "Month", "Day", "Dep. Time", "Sched. Dep. Time")
  )
```

Cross-referencing

• we can also refer to plots or tables in-text by typing @ followed by the label
  • e.g., This is some text describing @fig-flights-dec120.